number of cross overs per chromosome 1 - arabidopsis

Load libraries and the data

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Arabidopsis recombination landscape data is published in the following manuscript
http://www.nature.com/hdy/journal/v108/n4/full/hdy201195a.html.

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Supplemental information from above manuscript is downloaded and is in the following folder recombination_landscape

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box plot of number of cross overs in progeny of different parental crosses of arabidopsis

## No id variables; using all as measure variables
## Warning: Removed 893 rows containing non-finite values (stat_boxplot).

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fitting distribtuion to number of cross overs per chromosome

## Warning: package 'fitdistrplus' was built under R version 3.2.3
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful
## Warning in sqrt(diag(varcovar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(varcovar): diag(.) had 0 or NA entries; non-finite
## result is doubtful

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fitting distribtuion to number of cross overs per chromosome

##  chr     size num_plants   shape     rate   lambda    size       mu
##    1 30427671       6978 2.51999 1.469415       NA      NA       NA
##    1 30427671       6978      NA       NA 1.714961      NA       NA
##    1 30427671       6978      NA       NA       NA 6860232 1.714891

qq plots using fitted distributions